Inference

Abstract: Introduction * Information and Likelihood Theory: A Basis for Model Selection and Inference * Basic Use of the Information-Theoretic Approach * Formal Inference From More Than One Model: Multi-Model Inference (MMI) * Monte Carlo Insights and Extended Examples * Statistical Theory and Numerical Results * Summary

Abstract: History Conceptual Foundations Uses and Kinds of Inference The Logic of Content Analysis Designs Unitizing Sampling Recording Data Languages Constructs for Inference Analytical Techniques The Use of Computers Reliability Validity A Practical Guide

Abstract: Preface.PART I: OVERVIEW AND BASIC APPROACHES.Introduction.Missing Data in Experiments.Complete-Case and Available-Case Analysis, Including Weighting Methods.Single Imputation Methods.Estimation of Imputation Uncertainty.PART II: LIKELIHOOD-BASED APPROACHES TO THE ANALYSIS OF MISSING DATA.Theory of Inference Based on the Likelihood Function.Methods Based on Factoring the Likelihood, Ignoring the Missing-Data Mechanism.Maximum Likelihood for General Patterns of Missing Data: Introduction and Theory with Ignorable Nonresponse.Large-Sample Inference Based on Maximum Likelihood Estimates.Bayes and Multiple Imputation.PART III: LIKELIHOOD-BASED APPROACHES TO THE ANALYSIS OF MISSING DATA: APPLICATIONS TO SOME COMMON MODELS.Multivariate Normal Examples, Ignoring the Missing-Data Mechanism.Models for Robust Estimation.Models for Partially Classified Contingency Tables, Ignoring the Missing-Data Mechanism.Mixed Normal and Nonnormal Data with Missing Values, Ignoring the Missing-Data Mechanism.Nonignorable Missing-Data Models.References.Author Index.Subject Index.

Abstract: Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version 3.2, a major upgrade to the latest official release presented in 2003. The new version provides convergence diagnostics and allows multiple analyses to be run in parallel with convergence progress monitored on the fly. The introduction of new proposals and automatic optimization of tuning parameters has improved convergence for many problems. The new version also sports significantly faster likelihood calculations through streaming single-instruction-multiple-data extensions (SSE) and support of the BEAGLE library, allowing likelihood calculations to be delegated to graphics processing units (GPUs) on compatible hardware. Speedup factors range from around 2 with SSE code to more than 50 with BEAGLE for codon problems. Checkpointing across all models allows long runs to be completed even when an analysis is prematurely terminated. New models include relaxed clocks, dating, model averaging across time-reversible substitution models, and support for hard, negative, and partial (backbone) tree constraints. Inference of species trees from gene trees is supported by full incorporation of the Bayesian estimation of species trees (BEST) algorithms. Marginal model likelihoods for Bayes factor tests can be estimated accurately across the entire model space using the stepping stone method. The new version provides more output options than previously, including samples of ancestral states, site rates, site d(N)/d(S) rations, branch rates, and node dates. A wide range of statistics on tree parameters can also be output for visualization in FigTree and compatible software.